GreeNC

Gene information

This table contains information about coordinates, assembly and annotation regarding the lncRNA-transcribing gene. In details, it shows whether this this gene transcribes any protein-coding transcript.

Gene alias / name	Chrom.	Start	End	Source	Assembly	Species	Details
Taestivum_Traes_5BS_1EA5917AB Traes_5BS_1EA5917AB	ta_iwgsc_5bs_v1_2235786	844	22019	Phytozome	v2.2	Triticum_aestivum	Coding? Yes

Transcript features

This table shows how a lncRNA has been classified (high/low confidence) or whether it has been classified as pre-miRNA (go to FAQ for classification criteria). Besides, it displays the lncRNA length and sequence as well as information about the ORF, the coding potential calculated by the Coding Potential Calculator (CPC), and the folding energies calculated by RNAfold.

Transcript alias / name	Confidence	Pre-miRNA	Length	Sequence	Details
Taestivum_Traes_5BS_1EA5917AB.11 Traes_5BS_1EA5917AB.11 PAC:31768004	Low	No	1334		Get ORF Coding potential... Type: noncoding Potential: -1.127 Folding energies... MFEI: -26.927 AMFE: -0.632 GC content %: 42.579
Taestivum_Traes_5BS_1EA5917AB.12 Traes_5BS_1EA5917AB.12 PAC:31768005	High	No	306		Get ORF Coding potential... Type: noncoding Potential: -1.237 Folding energies... MFEI: -21.961 AMFE: -0.595 GC content %: 36.928

Matches to external databases

The lncRNAs from GreeNC have been analysed against the following databases: SwissProt, miRBase, Rfam, RepBase (RepeatMasker), NONCODE, and lncRNAdb. This table displays any association with these databases.

Transcript alias	Database	Version	Hit	Evalue
Taestivum_Traes_5BS_1EA5917AB.11	RepBase (RepeatMasker)	2014-01-31	hAT-9_SBi

Gene models

Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).